Alfonso Valencia

2020

• Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare

  Nature Digital Medicine

  D. Cirillo, S. Catuara-Solarz, C. Morey, E. Guney, L. Subirats, S. Mellino, A. Gigante, A. Valencia, M. José Rementeria, A. Santuccion Chadha, and N. Mavridis
• Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships

  Nature Communications

  J. Sánchez-Valle, H. Tejero, J. María Fernández, D. Juan, B. Urda-García, S. Capella-Gutierrez, F. Al-Shahrour, R. Tabarés-Seisdedos, A. Baudot, V. Pancaldi, and A. Valencia
• Pan-cancer analysis of whole genomes

  Nature

2019

• On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models

  Bioinformatics

  M. Ponce De Leon, I. Apaolaza, A. Valencia, and F. J. Planes
• Leveraging European infrastructures to access 1 million human genomes by 2022

  Nature Reviews Genetics

  G. Saunders, M. Baudis, R. Becker, S. Beltran, C. Béroud, E. Birney, C. Brooksbank, S. Brunak, M. Van den Bulcke, R. Drysdale, S. Capella-Gutierrez, P. Flicek, F. Florindi, P. Goodhand, I. Gut, J. Heringa, P. Holub, J. Hooyberghs, N. Juty, T. M. Keane, J. O. Korbel, I. Lappalainen, B. Leskošek, G. Matthijs, M. Th. Mayrhofer, A. Metspalu, A. Navarro, S. Newhouse, T. Nyrönen, A. Page, B. Persson, A. Palotie, H. Parkinson, J. Rambla, D. Salgado, E. Steinfelder, M. A. Swertz, A. Valencia, S. Varma, N. Blomberg, and S. Scollen
• PDBe-KB: a community-driven resource for structural and functional annotationsAbstract

  Nucleic Acids Research

  M. Varadi, J. Berrisford, M. Deshpande, S. S. Nair, A. Gutmanas, D. Armstrong, L. Pravda, B. Al-Lazikani, S. Anyango, G. J. Barton, K. Berka, T. Blundell, N. Borkakoti, J. Dana, S. Das, S. Dey, P. Di Micco, F. Fraternali, T. Gibson, M. Helmer-Citterich, D. Hoksza, L-C. Huang, R. Jain, H. Jubb, C. Kannas, N. Kannan, J. Koca, R. Krivak, M. Kumar, E. D. Levy, F. Madeira, M. S. Madhusudhan, H. J. Martell, S. MacGowan, J. E. McGreig, S. Mir, A. Mukhopadhyay, L. Parca, T. Paysan-Lafosse, L. Radusky, A. Ribeiro, L. Serrano, I. Sillitoe, G. Singh, P. Skoda, R. Svobodova, J. Tyzack, A. Valencia, E. Villasclar Fernandez, W. Vranken, M. Wass, J. Thornton, M. Sternberg, C. Orengo, and S. Velankar
• Patient Dossier: Healthcare queries over distributed resources

  PLoS computational biology

  M. Vázquez, and A. Valencia
• Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm

  Journal of Cheminformatics

  M. Pérez-Pérez, G. Pérez-Rodríguez, A. Blanco-Míguez, F. Fdez-Riverola, A. Valencia, M. Krallinger, and A. Lourenço
• The bio.tools registry of software tools and data resources for the life sciences

  Genome Biology

  J. Ison, H. Ienasescu, P. Chmura, E. Rydza, H. Ménager, M. Kalaš, V. Schwämmle, B. Grüning, N. Beard, R. Lopez, S. Duvaud, H. Stockinger, B. Persson, R. Svobodová Vařeková, T. Raček, J. Vondrášek, H. Peterson, A. Salumets, I. Jonassen, R. Hooft, T. Nyrönen, A. Valencia, S. Capella, J. Gelpí, F. Zambelli, B. Savakis, B. Leskošek, K. Rapacki, C. Blanchet, R. Jimenez, A. Oliveira, G. Vriend, O. Collin, J. van Helden, P. Løngreen, and S. Brunak
• BIOLITMAP: a web-based geolocated, temporal and thematic visualization of the evolution of bioinformatics publications

  Bioinformatics

  A. Bazaga, A. Valencia, and M-J. Rementeria